Various microbiota found in a living organism provide many crucial contributions to its host, including, for example, aiding digestion, aiding in the development of immune systems, and/or imparting resistance to pathogenic colonization. Even a slight fluctuation in the symbiotic balance between microbiota and its host may be deleterious to the host, possibly leading to a pathological condition. For example, perturbations in the human gut may lead to conditions such as Clostridium difficile infection or inflammatory bowel disease (IBD). The composition of a microbial community can undergo changes as a result of interactions between the microbiota and a host's immune and metabolic systems, and/or interactions between the microbiota and exogenous agents. In one example, human exposure to antibiotics is known to have both short-term and long-term effects on the composition of various host microbiota, including those of the gut. The ability to monitor various degrees of change in the microbiome is of utility in diagnosing and treating disease.